Limits...
Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

Hossain MA, Roslan HA - ScientificWorldJournal (2014)

Bottom Line: Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region.The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively.Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh ; Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.

ABSTRACT
beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

Show MeSH
Anolea, Qmean, and DSSP (define secondary structure of protein) obtained from the structural assessment by SWISS-MODEL workplace online software.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4129151&req=5

fig5: Anolea, Qmean, and DSSP (define secondary structure of protein) obtained from the structural assessment by SWISS-MODEL workplace online software.

Mentions: The SWISS-MODEL web server [29] was used to identify the 1now as template structure for homology modeling with 38.41% the target-template sequence identity. Another online server ModWeb Comparative Modeling Server version SVN.r1340:1348 M and I-TASSER [30] were also used for further modeling for appropriate model selection. To obtain an accurate homology model, it is very important that appropriate steps are built into the process to assess the quality of the model. Therefore, the accuracies of the predicted models were checked through a series of tests such as DFire [31], QMEAN [32], PROCHECK [33], WHAT_CHECK [34], VERIFY_3D [35], and also ModEval Model evaluation server [36]. A high quality predicted model was obtained from ModWeb comparative modeling web server through the analysis of predicted structures when compared with each other. However, the data for the rest of modeled structures are not shown. The Dfire energy and QMEAN score of best model were −716.03 and 0.511, respectively. The Ramachandran plot showed 88.1% of the residues in the most favoured region, 10.4% in the additional allowed region, 0.7% in the generally allowed region, and only 0.9% in the unfavourable region (Figure 4). Ramachandran Z-score is −0.669 indicating how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot and within expected ranges for a well-refined structure. None of the individual amino acid residues was in a bad packaging region. The structural average for the second-generation quality control value is within the normal range. All contacts average is −0.484 and Z-score is −2.49, which were within the normal ranges. The Anolea, QMean graph and DSSP (define secondary structure of protein) of modeled β-Hex-Sl obtained from the structural assessment by Swiss-model workplace are shown in Figure 5.


Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

Hossain MA, Roslan HA - ScientificWorldJournal (2014)

Anolea, Qmean, and DSSP (define secondary structure of protein) obtained from the structural assessment by SWISS-MODEL workplace online software.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4129151&req=5

fig5: Anolea, Qmean, and DSSP (define secondary structure of protein) obtained from the structural assessment by SWISS-MODEL workplace online software.
Mentions: The SWISS-MODEL web server [29] was used to identify the 1now as template structure for homology modeling with 38.41% the target-template sequence identity. Another online server ModWeb Comparative Modeling Server version SVN.r1340:1348 M and I-TASSER [30] were also used for further modeling for appropriate model selection. To obtain an accurate homology model, it is very important that appropriate steps are built into the process to assess the quality of the model. Therefore, the accuracies of the predicted models were checked through a series of tests such as DFire [31], QMEAN [32], PROCHECK [33], WHAT_CHECK [34], VERIFY_3D [35], and also ModEval Model evaluation server [36]. A high quality predicted model was obtained from ModWeb comparative modeling web server through the analysis of predicted structures when compared with each other. However, the data for the rest of modeled structures are not shown. The Dfire energy and QMEAN score of best model were −716.03 and 0.511, respectively. The Ramachandran plot showed 88.1% of the residues in the most favoured region, 10.4% in the additional allowed region, 0.7% in the generally allowed region, and only 0.9% in the unfavourable region (Figure 4). Ramachandran Z-score is −0.669 indicating how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot and within expected ranges for a well-refined structure. None of the individual amino acid residues was in a bad packaging region. The structural average for the second-generation quality control value is within the normal range. All contacts average is −0.484 and Z-score is −2.49, which were within the normal ranges. The Anolea, QMean graph and DSSP (define secondary structure of protein) of modeled β-Hex-Sl obtained from the structural assessment by Swiss-model workplace are shown in Figure 5.

Bottom Line: Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region.The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively.Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh ; Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.

ABSTRACT
beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

Show MeSH